Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  A TRANSITION FROM STRONG RIGHT-HANDED TO CANONICAL LEFT-HANDED SUPERCOILING IN A CONSERVED COILED COIL SEGMENT OF TRIMERIC AUTOTRANSPORTER ADHESINS - THE WILDTYPE STRUCTURE
 
Authors :  K. Zeth, B. Hernandez-Alvarez, A. N. Lupas
Date :  28 Apr 09  (Deposition) - 31 Mar 10  (Release) - 05 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Yada, Adhesin, Adhesion, Coiled Coil, Cell Adhesion, Cell Membrane, Cell Outer Membrane, Membrane, Plasmid, Virulence (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. H. Alvarez, M. Gruber, A. Ursinus, S. Dunin-Horkawicz, A. N. Lupas, K. Zeth
A Transition From Strong Right-Handed To Canonical Left-Handed Supercoiling In A Conserved Coiled-Coil Segment Of Trimeric Autotransporter Adhesins.
J. Struct. Biol. V. 170 236 2010
PubMed-ID: 20178846  |  Reference-DOI: 10.1016/J.JSB.2010.02.009

(-) Compounds

Molecule 1 - ADHESIN YADA
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: YADA STALK DOMAIN (RESIDUES 299-362)
    Gene: YADA
    Organism Scientific: YERSINIA ENTEROCOLITICA
    Organism Taxid: 630

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3H7X)

(-) Sites  (0, 0)

(no "Site" information available for 3H7X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H7X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H7X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H7X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H7X)

(-) Exons   (0, 0)

(no "Exon" information available for 3H7X)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:57
 aligned with YADA2_YEREN | P0C2W0 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:57
                                   310       320       330       340       350       
          YADA2_YEREN   301 SSHTLKTANSYTDVTVSNSTKKAIRESNQYTDHKFHQLDNRLDKLDTRVDKGLASSA 357
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                 3h7x A 301 SSHTLKTANSYTDVTVSNSTKKAIRESNQYTDHKFHQLDNRLDKLDTRVDKGLASSA 357
                                   310       320       330       340       350       


Chain B from PDB  Type:PROTEIN  Length:51
 aligned with YADA2_YEREN | P0C2W0 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:51
                                   312       322       332       342       352 
          YADA2_YEREN   303 HTLKTANSYTDVTVSNSTKKAIRESNQYTDHKFHQLDNRLDKLDTRVDKGL 353
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                 3h7x B 303 HTLKTANSYTDVTVSNSTKKAIRESNQYTDHKFHQLDNRLDKLDTRVDKGL 353
                                   312       322       332       342       352 


Chain C from PDB  Type:PROTEIN  Length:51
 aligned with YADA2_YEREN | P0C2W0 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:51
                                   313       323       333       343       353 
          YADA2_YEREN   304 TLKTANSYTDVTVSNSTKKAIRESNQYTDHKFHQLDNRLDKLDTRVDKGLA 354
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                 3h7x C 304 TLKTANSYTDVTVSNSTKKAIRESNQYTDHKFHQLDNRLDKLDTRVDKGLA 354
                                   313       323       333       343       353 


Chain D from PDB  Type:PROTEIN  Length:54
 aligned with YADA2_YEREN | P0C2W0 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:54
                                   313       323       333       343       353    
          YADA2_YEREN   304 TLKTANSYTDVTVSNSTKKAIRESNQYTDHKFHQLDNRLDKLDTRVDKGLASSA 357
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                 3h7x D 304 TLKTANSYTDVTVSNSTKKAIRESNQYTDHKFHQLDNRLDKLDTRVDKGLASSA 357
                                   313       323       333       343       353    


Chain E from PDB  Type:PROTEIN  Length:53
 aligned with YADA2_YEREN | P0C2W0 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:53
                                   311       321       331       341       351   
          YADA2_YEREN   302 SHTLKTANSYTDVTVSNSTKKAIRESNQYTDHKFHQLDNRLDKLDTRVDKGLA 354
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 3h7x E 302 SHTLKTANSYTDVTVSNSTKKAIRESNQYTDHKFHQLDNRLDKLDTRVDKGLA 354
                                   311       321       331       341       351   


Chain F from PDB  Type:PROTEIN  Length:53
 aligned with YADA2_YEREN | P0C2W0 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:53
                                   311       321       331       341       351   
          YADA2_YEREN   302 SHTLKTANSYTDVTVSNSTKKAIRESNQYTDHKFHQLDNRLDKLDTRVDKGLA 354
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 3h7x F 302 SHTLKTANSYTDVTVSNSTKKAIRESNQYTDHKFHQLDNRLDKLDTRVDKGLA 354
                                   311       321       331       341       351
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3H7X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H7X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H7X)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (YADA2_YEREN | P0C2W0)
molecular function
    GO:0005518    collagen binding    Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019867    outer membrane    The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3h7x)
 
  Sites
(no "Sites" information available for 3h7x)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3h7x)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3h7x
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  YADA2_YEREN | P0C2W0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  YADA2_YEREN | P0C2W0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        YADA2_YEREN | P0C2W0: 3h7z

(-) Related Entries Specified in the PDB File

3h7z